Antibiotic resistance genes (ARGs) have accelerated microbial threats to human health in the last decade. Many genes can confer resistance, but evaluating the relative health risks of ARGs is complex. Factors such as the abundance, propensity for lateral transmission and ability of ARGs to be expressed in pathogens are all important. Here, an analysis at the metagenomic level from various habitats (6 types of habitats, 4572 samples) detects 2561 ARGs that collectively conferred resistance to 24 classes of antibiotics. We quantitatively evaluate the health risk to humans, defined as the risk that ARGs will confound the clinical treatment for pathogens, of these 2561 ARGs by integrating human accessibility, mobility, pathogenicity and clinical availability. Our results demonstrate that 23.78% of the ARGs pose a health risk, especially those which confer multidrug resistance. We also calculate the antibiotic resistance risks of all samples in four main habitats, and with machine learning, successfully map the antibiotic resistance threats in global marine habitats with over 75% accuracy. Our novel method for quantitatively surveilling the health risk of ARGs will help to manage one of the most important threats to human and animal health.

The occurrence of parallel speciation strongly implies the action of natural selection. However, it is unclear how general a phenomena parallel speciation is since it was only shown in a small number of animal species. In particular, the adaptive process and mechanisms underlying the process of parallel speciation remain elusive. Here, we used an integrative approach incorporating population genomics, common garden, and crossing experiments to investigate parallel speciation of the wild rice species Oryza nivara from O. rufipogon . We demonstrated that O. nivara originated multiple times from different O. rufipogon populations and revealed that different O. nivara populations have evolved similar phenotypes under divergent selection, a reflection of recurrent local adaptation of ancient O. rufipogon populations to dry habitats. Almost completed premating isolation was detected between O. nivara and O. rufipogon in the absence of any postmating barriers between and within these species. These results suggest that flowering time is a “magic” trait that contributes to both local adaptation and reproductive isolation in the origin of wild rice species. Our study thus demonstrates a convincing case of parallel ecological speciation as a consequence of adaptation to new environments.

Depression and obesity have high concurrence within individuals, which may be explained by sharing the same risk factors, including disruption of the intestinal microbiota. However, evidence that delineated the causal connections is extremely scarce. Methods: Mice lacking fat mass- and obesity-associated gene ( Fto ) were generated. Fto -deficient and wild-type control mice were subjected to novel conditions with or without chronic unpredictable mild stress (CUMS) for 6 weeks. Some mice were treated with antibiotics via their drinking water for 6 weeks in order to deplete their microbiota. Behavioral tests were performed to evaluate anxiety- and depression-like behaviors. 16S rRNA amplicon and metagenomic sequencing were employed to analyse fecal microbiota. Plasma levels of inflammatory cytokines and lipopolysaccharides (LPS) were also compared. Results: Deletion of Fto led to lower body weight and decreased anxiety- and depression-like behaviors, Fto +/- mice were also less susceptible to stress stimulation, highlighting the essential role of Fto in pathogenesis of depression. With regard to gut microbiota, Fto deficiency mice harbored specific bacterial signature of suppressing inflammation, characterized with higher abundance of Lactobacillus , lower Porphyromonadaceae and Helicobacter . Critically, behavioral alterations of Fto +/- mice are mediated by shift in gut microbiota, as such changes can be partially attenuated using antibiotics. Exposure to CUMS increased serum IL-6 level while Fto deficiency reduced its level, which may be explained by a lower LPS concentration. Conclusion: Together, our findings uncover the roles of Fto on depression and provide insights into microbiota-related biological mechanisms underlying the association between obesity and depression.